Install new motor mounts. They should just be pucks and easily swapped with a jack. I've changed a few that were splitting and the before and after were remarkable.
It sounds dumb, but being vibrated like that on a several hour road trip is exhausting for your muscles and joints.
As far as flexing is concerned, it's real. Drive one wheel up on a curb and hear the body creak in the process. Maybe not on a shorty, but a full sized bus will do it for sure.
Follow christopher's advice. Those seals leak and typically by the time you notice it, it's already a rusty mess that is super difficult to fix. I'd have to look at what you have in person to say for sure, but I would think you could cut that out, box around your unit with steel angle, weld it all tight, and be okay. But like I said, without being there, I'm not advising it.